Even as federal inspectors repeatedly warned that patient wait lists were having a detrimental impact on care, the troubled Veterans Affairs health system handed out $108.7 million in bonuses to executives and employees the past three years, an Asbury Park Press investigation found.

The top bonuses went to top executives in the Veterans Health Administration, which has come under fire for what its Office of Inspector General called “systemic patient safety issues” that may have led to wrongful deaths. Last year, the top bonuses — of $21,000, $17,000 and $13,000 — went to medical and dental officers in San Diego, according to the Press’ review of payroll data from the Office of Personnel Management.

Those figures are down from the year before, when the three top bonuses each awarded were $62,895, according to pay data.

View a list of bonuses by agency and individual at www.DataUniverse.com, the Press’ public records website. Look under “What’s New” for a link to federal employee salaries.

Meanwhile, patient wait times were a well-documented problem at the VA. Since 2005, the agency’s inspector general issued 18 interim reports “that identified, at both the national and local levels, deficiencies in scheduling resulting in lengthy waiting times and the negative impact on patient care,” according to a report last month.

Rep. Frank LoBiondo, R-N.J., who represents portions of southern Ocean County, called the VA’s culture of rewarding employees while patients waited for care “outrageous.”

“It hasn’t been working and the more information that comes to light, the more outrageous it is. I know everyone has to be innocent until proven guilty, but I think criminal pursuit should take place here,” LoBiondo said. “You can’t have veterans die and just say it was mismanagement.”

Bonuses for New Jersey VA health care employees pale in comparison to the rest of the nation. In 2013, 40 employees received bonuses averaging $1,848, as part of $74,000 in rewards. In 2012, a total of $83,350 was awarded to 37 employees. The bonuses ranged from $1,065 to $5,000, but averaged $2,253 that year. The Press examined bonuses that exceeded $1,000. Rewards below that can be paid through days off and other non-monetary perks, according to the Office of Personnel Management.

Since the problems at the VA came to light, decorated war veteran Eric Shinseki resigned as VA secretary and the agency put a hold on employee bonuses for 2014.

Lawmakers went a step further Tuesday, unanimously passing a bill in the House of Representatives that would suspend employee bonuses through 2016, among other measures. The VA acknowledged that employees did not appropriately place veterans on wait lists and leadership “significantly understated” wait times, a factor considered in salary increases and bonuses.

“Here’s what the systemic problem is when you look at it all. The way they’re measuring success is by a metric that even the (Inspector General) can’t tell us how they came up with the numbers,” said Rep. Jon Runyan, R-N.J., who represents parts of Ocean County. “That’s where these secret lists come in to factor, because if they’re not in the computer system, they’re not on the clock for getting that patient seen, and so they’re cooking the books by not putting them in the computer system. Now they can get their bonuses on the back end.”

More than 57,000 veterans across the country have waited 90 days to see a doctor, the VA said. An audit found 81 VA sites required further review to determine the “extent of issues” in scheduling and management practices. The VA campus in Lyons is on that list, with 379 patients waiting longer than 90 days to see a doctor, according to officials.

“We are awaiting further information regarding the details about why the Lyons Campus was selected for further review and about what will be the next steps of the review process,” VA spokeswoman Sandy Warren wrote in an email. “We are reviewing productivity of clinics and assessing their availability to see additional patients.”

Nine Lyons officials were awarded bonuses last year totaling $17,925, according to the personnel management data.

The payroll data did not show a clear link between hospitals chosen by the VA for further review and bonus amounts. But in Phoenix, where a whistle blower former employee revealed a pattern of patient wait lists being manipulated, top executive Sharon Helman was directed to repay her bonus of $9,345. Helman, who last year earned a salary of $169,900, ranked 10th on the list of executive bonuses.

LoBiondo suggested that Helman may not be the only one.

“Instead of somebody figuring out what bonuses to give out, they should have been figuring out how to get everything staffed up so that these problems did not occur. It is outrageous,” he said. “They ought to somehow demand to get the money back.”